• 【一种应用于微血管血流多尺度模型的全局敏感性分析方法。】 复制标题 收藏 收藏
    DOI:10.1080/10255842.2020.1793964 复制DOI
    作者列表:Possenti L,Di Gregorio S,Casagrande G,Costantino ML,Rancati T,Zunino P
    BACKGROUND & AIMS: :A global sensitivity analysis of a multiscale computational model of microvascular flow is presented. A total of 140 simulations have been completed and analyzed varying 6 input parameters and considering their effects on 7 output variables. Interestingly, the vascular network topology has been found as a determinant factor for both vasculature-related and interstitium-related quantities. Regarding the firsts, the vascular network topology has obtained a score of 5.5/6 and 6/6 for average and spatial distribution respectively (where 6 is the maximum and 1 is the minimum). On the other hand, considering interstitium-related quantities, the score is 4/6 and 5/6 for average and spatial distribution respectively. These results suggest that the network topology has a significant influence on the outcome of the computational analysis.
    背景与目标: : 提出了微血管血流多尺度计算模型的全局灵敏度分析。总共完成了140个模拟,并分析了6个输入参数的变化,并考虑了它们对7个输出变量的影响。有趣的是,已发现血管网络拓扑结构是脉管系统相关量和间质相关量的决定因素。关于第一个,血管网络拓扑分别获得了平均和空间分布的5.5/6和6/6的分数 (其中6是最大值,1是最小值)。另一方面,考虑到间质相关的数量,得分分别为平均和空间分布的4/6和5/6。这些结果表明,网络拓扑结构对计算分析的结果有重大影响。
  • 2 Entropy Evolution in Consensus Networks. 复制标题 收藏 收藏

    【共识网络中的熵演化。】 复制标题 收藏 收藏
    DOI:10.1038/s41598-017-01615-5 复制DOI
    作者列表:Fu S,Shi G,Petersen IR,James MR
    BACKGROUND & AIMS: :We investigate the evolution of the network entropy for consensus dynamics in classical and quantum networks. We show that in the classical case, the network differential entropy is monotonically non-increasing if the node initial values are continuous random variables. While for quantum consensus dynamics, the network's von Neumann entropy is in contrast non-decreasing. In light of this inconsistency, we compare several distributed algorithms with random or deterministic coefficients for classical or quantum networks, and show that quantum algorithms with deterministic coefficients are physically related to classical algorithms with random coefficients.
    背景与目标: : 我们研究了经典网络和量子网络中共识动力学的网络熵的演变。我们证明,在经典情况下,如果节点初始值是连续随机变量,则网络微分熵是单调不增加的。而对于量子共识动力学,网络的冯·诺依曼熵却没有减少。鉴于这种不一致,我们比较了经典或量子网络的几种具有随机或确定性系数的分布式算法,并表明具有确定性系数的量子算法与具有随机系数的经典算法在物理上相关。
  • 【肌肉骨骼系统的多尺度建模。】 复制标题 收藏 收藏
    DOI:10.1146/annurev-bioeng-071516-044555 复制DOI
    作者列表:Jung GS,Buehler MJ
    BACKGROUND & AIMS: :Multiscale modeling of muscular-skeletal systems-the materials and structures that help organisms support themselves and move-is a rapidly growing field of study that has contributed key elements to the understanding of these systems, especially from a multiscale perspective. The systems, including materials such as bone and muscle, have hierarchical structures ranging from the nano- to the macroscale, and it is difficult to understand their macroscopic behaviors, both physiological and pathological, without knowledge of their hierarchical structures and properties. In this review, we discuss the methods of multiscale modeling. Through a series of case studies about key materials in muscular-skeletal systems, we describe how different methods can bridge the gap between hierarchical structures and their roles in the systems' mechanical properties. In particular, we emphasize the importance of the quality of minerals in bone. Finally, we discuss biomimetic material designs facilitated by additive manufacturing technology.
    背景与目标: : 肌肉骨骼系统的多尺度建模-帮助生物支撑自己和移动的材料和结构-是一个快速发展的研究领域,为理解这些系统做出了关键因素,特别是从多尺度的角度来看。包括骨骼和肌肉等材料在内的系统具有从纳米到宏观的层次结构,如果不了解其层次结构和特性,就很难理解其宏观行为,包括生理和病理行为。在这篇综述中,我们讨论了多尺度建模的方法。通过一系列有关肌肉骨骼系统中关键材料的案例研究,我们描述了不同的方法如何弥合层次结构之间的鸿沟及其在系统机械性能中的作用。我们特别强调骨骼中矿物质质量的重要性。最后,我们讨论了增材制造技术促进的仿生材料设计。
  • 【配体构型熵与蛋白质结合。】 复制标题 收藏 收藏
    DOI:10.1073/pnas.0610494104 复制DOI
    作者列表:Chang CE,Chen W,Gilson MK
    BACKGROUND & AIMS: :The restriction of a small molecule's motion on binding to a protein causes a loss of configurational entropy, and thus a penalty in binding affinity. Some energy models used in computer-aided ligand design neglect this entropic penalty, whereas others account for it based on an expected drop in the number of accessible rotamers upon binding. However, the validity of the physical assumptions underlying the various approaches is largely unexamined. The present study addresses this issue by using Mining Minima calculations to analyze the association of amprenavir with HIV protease. The computed loss in ligand configurational entropy is large, contributing approximately 25 kcal/mol (4.184 kJ/kcal) to DeltaG degrees. Most of this loss results from narrower energy wells in the bound state, rather than a drop in the number of accessible rotamers. Coupling among rotation/translation and internal degrees of freedom complicates the decomposition of the entropy change into additive terms. The results highlight the potential to gain affinity by designing conformationally restricted ligands and have implications for the formulation of energy models for ligand scoring.
    背景与目标: : 小分子对与蛋白质结合的运动的限制会导致构型熵的损失,从而降低结合亲和力。计算机辅助配体设计中使用的某些能量模型忽略了这种熵损失,而其他模型则基于结合后可访问的旋转异构体数量的预期下降来解释它。但是,各种方法所依据的物理假设的有效性在很大程度上尚未得到检验。本研究通过使用Mining Minima计算来分析氨普瑞韦与HIV蛋白酶的关联来解决此问题。计算的配体构型熵的损失很大,对DeltaG度贡献约25 kcal/mol (4.184 kJ/kcal)。这种损失的大部分是由于约束状态下较窄的能量阱造成的,而不是可访问的旋转异构体数量的减少。旋转/平移和内部自由度之间的耦合使熵变化分解为加法项变得复杂。结果强调了通过设计构象受限的配体来获得亲和力的潜力,并对配体评分的能量模型的制定有影响。
  • 【机器人沉积具有多种结构和多尺度孔隙率的羟基磷灰石模型支架,用于骨组织工程。】 复制标题 收藏 收藏
    DOI:10.1002/jbm.a.31072 复制DOI
    作者列表:Dellinger JG,Cesarano J 3rd,Jamison RD
    BACKGROUND & AIMS: :Model hydroxyapatite (HA) scaffolds with porosities spanning multiple length scales were fabricated by robocasting, a solid freeform fabrication technique based on the robotic deposition of colloidal pastes. Scaffolds of various architectures including periodic, radial, and superlattice structures were constructed. Macropores (100-600 microm) were designed by controlling the arrangement and spacing between rods of HA. Micropores (1-30 microm) and submicron pores (less than 1 microm) were produced within the rods by including polymer microsphere porogens in the HA pastes and by controlling the sintering of the scaffolds. These model scaffolds may be used to systematically study the effects of scaffold porosity on bone ingrowth processes both in vitro and in vivo.
    背景与目标: : 通过robocasting制造了具有多个长度尺度的孔隙率的羟基磷灰石 (HA) 模型支架,robocasting是一种基于胶体糊剂机器人沉积的固体自由形式制造技术。构建了各种体系结构的支架,包括周期性,径向和超晶格结构。通过控制HA杆之间的排列和间距来设计大孔 (100-600微米)。通过在HA糊中加入聚合物微球致孔剂并控制支架的烧结,在棒内产生微孔 (1-30微米) 和亚微米孔 (小于1微米)。这些模型支架可用于系统地研究支架孔隙率对体外和体内骨向内生长过程的影响。
  • 【隔夜脉搏血氧饱和度数据的近似熵在阻塞性睡眠呼吸暂停综合征诊断中的效用。】 复制标题 收藏 收藏
    DOI:10.1109/TBME.2006.883821 复制DOI
    作者列表:Hornero R,Alvarez D,Abásolo D,del Campo F,Zamarrón C
    BACKGROUND & AIMS: :Approximate entropy (ApEn) is a family of statistics introduced as a quantification of regularity in time series without any a priori knowledge about the system generating them. The aim of this preliminary study was to assess whether a time series analysis of arterial oxygen saturation (SaO2) signals from overnight pulse oximetry by means of ApEn could yield essential information on the diagnosis of obstructive sleep apnea (OSA) syndrome. We analyzed SaO2 signals from 187 subjects: 111 with a positive diagnosis of OSA and 76 with a negative diagnosis of OSA. We divided our data in a training set (44 patients with OSA Positive and 30 patients with OSA Negative) and a test set (67 patients with OSA Positive and 46 patients with OSA Negative). The training set was used for algorithm development and optimum threshold selection. Results showed that recurrence of apnea events in patients with OSA determined a significant increase in ApEn values. This method was assessed prospectively using the test dataset, where we obtained 82.09% sensitivity and 86.96% specificity. We conclude that ApEn analysis of SaO2 from pulse oximetric recording could be useful in the study of OSA.
    背景与目标: : 近似熵 (ApEn) 是作为时间序列中规律性的量化而引入的统计数据族,而没有任何有关生成它们的系统的先验知识。这项初步研究的目的是评估通过ApEn对隔夜脉搏血氧饱和度 (SaO2) 信号进行的时间序列分析是否可以提供有关阻塞性睡眠呼吸暂停 (OSA) 综合征诊断的重要信息。我们分析了来自187名受试者的SaO2信号: 111名OSA诊断为阳性,76名OSA诊断为阴性。我们将数据分为训练集 (44例OSA阳性和30例OSA阴性) 和测试集 (67例OSA阳性和46例OSA阴性)。训练集用于算法开发和最佳阈值选择。结果显示,OSA患者呼吸暂停事件的复发决定了ApEn值的显着增加。使用测试数据集对该方法进行了前瞻性评估,其中我们获得了82.09% 敏感性和86.96% 特异性。我们得出的结论是,脉搏血氧记录对SaO2的ApEn分析可能对OSA的研究有用。
  • 【更正: 使用样本熵方法对4英尺类型的足底压力中心的功能差异进行探索性研究。】 复制标题 收藏 收藏
    DOI:10.1007/s11517-020-02145-5 复制DOI
    作者列表:Mei Z,Ivanov K,Zhao G,Li H,Wang L
    BACKGROUND & AIMS: :In the original publication of the article the affiliation of Kamen Ivanov was inaccurate. The correct affiliation of Kamen Ivanov is given below.
    背景与目标: : 在文章的原始出版物中,Kamen Ivanov的隶属关系不准确。以下给出了假面伊万诺夫的正确隶属关系。
  • 【Shannon熵应用于事件相关功能磁共振成像时间序列分析。】 复制标题 收藏 收藏
    DOI:10.1016/s1053-8119(03)00306-9 复制DOI
    作者列表:de Araujo DB,Tedeschi W,Santos AC,Elias J Jr,Neves UP,Baffa O
    BACKGROUND & AIMS: :Event-related functional magnetic resonance imaging (ER-fMRI) refers to the blood oxygen level-dependent (BOLD) signal in response to a short stimulus followed by a long period of rest. These paradigms have become more popular in the last few years due to some advantages over standard block techniques. Most of the analysis of the time series generated in such exams is based on a model of specific hemodynamic response function. In this paper we propose a new method for the analysis of ER-fMRI based in a specific aspect of information theory: the entropy of a signal using the Shannon formulation, which makes no assumption about the shape of the response. The results show the ability to discriminate between activated and resting cerebral regions for motor and visual stimuli. Moreover, the results of simulated data show a more stable pattern of the method, if compared to typical algorithms, when the signal to noise ratio decreases.
    背景与目标: : 事件相关的功能磁共振成像 (ER-fMRI) 是指对短暂刺激,随后长时间休息的血氧水平依赖性 (BOLD) 信号。由于与标准块技术相比具有一些优势,这些范例在最近几年变得越来越流行。在此类检查中生成的时间序列的大多数分析都是基于特定血液动力学响应函数的模型。在本文中,我们提出了一种基于信息论的特定方面的ER-fMRI分析的新方法: 使用Shannon公式的信号熵,该方法不对响应的形状进行假设。结果表明,能够区分运动和视觉刺激的激活和静止大脑区域。此外,当信噪比降低时,如果与典型算法相比,模拟数据的结果显示出该方法的更稳定模式。
  • 【通过对心脏周期变化的语调熵分析,得出了自主功能随年龄的比较量表。】 复制标题 收藏 收藏
    DOI:10.1007/s00421-006-0275-9 复制DOI
    作者列表:Amano M,Oida E,Moritani T
    BACKGROUND & AIMS: :Tremendous numbers of heart rate variability studies have aimed to elucidate age-associated alterations of autonomic function in the past decades. However, the studies, far from clarifying ageing mechanisms, fell into confusion by a lack of common scales. The purpose of this study is to show a possibility to establish a comparative scale of autonomic function through a method, tone-entropy (T-E) analysis on heart period variation, whose validity has been already examined on typical physiological cases (Oida et al. in J Appl Physiol 82:1794-1801, 1997; Oida et al. in J Gerontol 54A:M219-M224, 1999a; Oida et al. in Acta Physiol Scand 165:129-134, 1999b; Oida et al. in Acta Physiol Scand 165:421-422, 1999c; Amano et al. in Eur J Appl Physiol 94:602-610, 2005). In this study, 276 subjects from teens to seventies were examined at rest by T-E analysis together with conventional time and frequency domain analyses. The tone (negativity represents vagal predominance) became significantly high [-0.174 +/- 0.026 (teens) to -0.024 +/- 0.004 (seventies), P < 0.05 for one-way ANOVA], and the entropy (total autonomic activity), significantly low [4.40 +/- 0.12 (teens) to 2.90 +/- 0.09 bit (seventies), P < 0.05] with advancing age. The result, plotted in 2-D T-E space, showed that the ageing traced a curvi-linear relation from right-bottom to left-top, and was consistent with previously studied typical physiological cases. The conventional analyses showed almost the same autonomic reduction as T-E did, but failed in detecting delicate alteration of autonomic balance. The results, showing that autonomic activity reduced in both pathways impairing vagal predominance significantly with ageing, suggested a possibility to assess autonomic function in 2-D T-E space in a comparative way.
    背景与目标: : 在过去的几十年中,大量的心率变异性研究旨在阐明与年龄相关的自主神经功能变化。然而,这些研究非但没有阐明衰老机制,反而因缺乏共同的量表而陷入混乱。这项研究的目的是通过一种方法,即心脏周期变化的音调熵 (t-e) 分析,表明建立自主功能的比较量表的可能性,该方法的有效性已经在典型的生理情况下进行了检验 (Oida等。在J Appl Physiol 82:1794-1801中,1997; Oida等人在J Gerontol 54A:M219-M224,1999a; Oida等人在《物理学报》Scand 165:129-134,1999b; Oida等人在《物理学报》Scand 165:421-422,1999c; Amano等人在Eur J Appl Physiol 94:602-610,2005)。在这项研究中,通过t-e分析以及常规的时域和频域分析,对276名青少年至70岁的受试者进行了静息检查。音调 (负性代表迷走神经占优势) 变得显著高 [-0.174 +/- 0.026 (青少年) 至-0.024 +/- 0.004 (七十年代),P <0.05单因素方差分析] 和熵 (总自主活动),随着年龄的增长,显着降低 [4.40/- 0.12 (青少年) 至2.90/- 0.09位 (70岁),P <0.05]。在2-D T-E空间中绘制的结果表明,衰老从右下到左上具有曲线线性关系,并且与先前研究的典型生理情况一致。常规分析显示出与t-e几乎相同的自主神经降低,但未能检测到自主神经平衡的微妙变化。结果表明,随着年龄的增长,两种途径的自主神经活动均降低,从而显着损害了迷走神经的优势,这表明有可能以比较的方式评估2-D t-e空间中的自主神经功能。
  • 【关于在心血管控制分析中计算样本熵的局部版本的相关性。】 复制标题 收藏 收藏
    DOI:10.1109/TBME.2018.2852713 复制DOI
    作者列表:Porta A,Bari V,De Maria B,Cairo B,Vaini E,Malacarne M,Pagani M,Lucini D
    BACKGROUND & AIMS: OBJECTIVE:Traditional definition of sample entropy (SampEn), here referred to as global SampEn (GSampEn), provides a conditional entropy estimate that blurs the local statistical properties of the time series. We hypothesized that a local version of SampEn (LSampEn) might be more powerful in the presence of determinism than GSampEn. METHODS:LSampEn was computed by calculating the probability of the current sample conditioned on each reference pattern and averaging it over all reference patterns. The improved ability of LSampEn compared to GSampEn was demonstrated by simulating deterministic periodic, deterministic chaotic, and linear stochastic dynamics corrupted by additive noise and over real cardiovascular variability series recorded from 16 healthy subjects (max-min age range: 22-58 years) during incremental bicycle ergometer exercise. RESULTS:We found that: i) LSampEn is more robust in describing deterministic periodic or nonlinear features in the presence of additive noise than GSampEn, ii) in association with a surrogate approach, LSampEn is more powerful in detecting nonlinear dynamics than GSampEn, iii) LSampEn and GSampEn are equivalent in the presence of stochastic linear dynamics, and iv) only LSampEn can detect the decrease of complexity of heart period variability during bicycle exercise being a likely hallmark of sympathetic activation. CONCLUSION:LSampEn preserves the GSampEn capability in characterizing the complexity of short sequences but improves its reliability in the presence of deterministic patterns featuring sharp state transitions and nonlinear dynamics. SIGNIFICANCE:Variations of complexity can be measured with a greater statistical power over short series using LSampEn, especially when nonlinear features are present.
    背景与目标:
  • 【美国哺乳动物保护区连通性的多尺度网络分析。】 复制标题 收藏 收藏
    DOI:10.1111/j.1523-1739.2010.01558.x 复制DOI
    作者列表:Minor ES,Lookingbill TR
    BACKGROUND & AIMS: :Protected areas must be close, or connected, enough to allow for the preservation of large-scale ecological and evolutionary processes, such as gene flow, migration, and range shifts in response to climate change. Nevertheless, it is unknown whether the network of protected areas in the United States is connected in a way that will preserve biodiversity over large temporal and spatial scales. It is also unclear whether protected-area networks that function for larger species will function for smaller species. We assessed the connectivity of protected areas in the three largest biomes in the United States. With methods from graph theory--a branch of mathematics that deals with connectivity and flow--we identified and measured networks of protected areas for three different groups of mammals. We also examined the value of using umbrella species (typically large-bodied, far-ranging mammals) in designing large-scale networks of protected areas. Although the total amount of protected land varied greatly among biomes in the United States, overall connectivity did not. In general, protected-area networks were well connected for large mammals but not for smaller mammals. Additionally, it was not possible to predict connectivity for small mammals on the basis of connectivity for large mammals, which suggests the umbrella species approach may not be an appropriate design strategy for conservation networks intended to protect many species. Our findings indicate different strategies should be used to increase the likelihood of persistence for different groups of species. Strategic linkages of existing lands should be a conservation priority for smaller mammals, whereas conservation of larger mammals would benefit most from the protection of more land.
    背景与目标: : 保护区必须紧密或相连,以允许保存大规模的生态和进化过程,例如应对气候变化的基因流,迁移和范围转移。尽管如此,尚不清楚美国的保护区网络是否以能够在较大的时间和空间尺度上保护生物多样性的方式连接在一起。还不清楚对较大物种起作用的保护区网络是否会对较小物种起作用。我们评估了美国三个最大生物群落中保护区的连通性。利用图论的方法 (涉及连通性和流量的数学分支),我们确定并测量了三组不同哺乳动物的保护区网络。我们还研究了在设计大规模保护区网络时使用伞形物种 (通常是大型,范围广泛的哺乳动物) 的价值。尽管美国生物群落之间受保护土地的总量差异很大,但总体连通性却没有。通常,大型哺乳动物的保护区网络连接良好,而小型哺乳动物则没有。此外,无法根据大型哺乳动物的连通性来预测小型哺乳动物的连通性,这表明伞形物种方法可能不是旨在保护许多物种的保护网络的适当设计策略。我们的发现表明,应使用不同的策略来增加不同物种群体持久性的可能性。现有土地的战略联系应该是较小哺乳动物的保护优先事项,而较大哺乳动物的保护将从更多土地的保护中受益最大。
  • 【基于多频带熵的特征提取方法,用于基于interictal iEEG中高频成分的癫痫焦点自动识别。】 复制标题 收藏 收藏
    DOI:10.1038/s41598-020-62967-z 复制DOI
    作者列表:Akter MS,Islam MR,Iimura Y,Sugano H,Fukumori K,Wang D,Tanaka T,Cichocki A
    BACKGROUND & AIMS: :Presurgical investigations for categorizing focal patterns are crucial, leading to localization and surgical removal of the epileptic focus. This paper presents a machine learning approach using information theoretic features extracted from high-frequency subbands to detect the epileptic focus from interictal intracranial electroencephalogram (iEEG). It is known that high-frequency subbands (>80 Hz) include important biomarkers such as high-frequency oscillations (HFOs) for identifying epileptic focus commonly referred to as the seizure onset zone (SOZ). In this analysis, the multi-channel interictal iEEG signals were splitted into segments and each segment was decomposed into multiple high-frequency subbands. The different types of entropy were calculated for each of the subbands and the sparse linear discriminant analysis (sLDA) was applied to select the prominent entropy features. Due to the imbalance of SOZ and non-SOZ channels in iEEG data, the use of machine learning techniques is always tricky. To deal with the imbalanced learning problem, an adaptive synthetic oversampling approach (ADASYN) with radial basis function kernel-based SVM was used to detect the focal segments. Finally, the epileptic focus was identified based on detection of focal segments on SOZ and non-SOZ channels. Eight patients were examined to observe the efficiency of the automatic detector. The experimental results and statistical tests indicate that the proposed automatic detector can identify the epileptic focus accurately and efficiently.
    背景与目标: : 对局灶性模式进行分类的术前研究至关重要,从而导致癫痫灶的定位和手术切除。本文提出了一种机器学习方法,该方法使用从高频子带中提取的信息理论特征来检测发作期颅内脑电图 (iEEG) 中的癫痫灶。众所周知,高频子带 (>80 hz) 包括重要的生物标志物,例如用于识别癫痫灶的高频振荡 (HFOs),通常称为癫痫发作区 (SOZ)。在此分析中,将多通道interictal iEEG信号分成多个段,并将每个段分解为多个高频子带。为每个子带计算不同类型的熵,并应用稀疏线性判别分析 (sLDA) 来选择突出的熵特征。由于iEEG数据中SOZ和非SOZ通道的不平衡,机器学习技术的使用总是很棘手。为了解决不平衡学习问题,使用了具有基于径向基函数核的SVM的自适应综合过采样方法 (ADASYN) 来检测焦点片段。最后,根据对SOZ和非SOZ通道上的灶段的检测,确定了癫痫灶。对八名患者进行了检查,以观察自动检测器的效率。实验结果和统计测试表明,所提出的自动检测器可以准确有效地识别癫痫灶。
  • 【病毒衣壳上DNA的熵、能量和弯曲。】 复制标题 收藏 收藏
    DOI:10.1016/j.bpj.2013.04.006 复制DOI
    作者列表:Ben-Shaul A
    BACKGROUND & AIMS: :Inspired by novel single-molecule and bulk solution measurements, the physics underlying the forces and pressures involved in DNA packaging into bacteriophage capsids became the focus of numerous recent theoretical models. These fall into two general categories: Continuum-elastic theories (CT), and simulation studies-mostly of the molecular dynamics (MD) genre. Both types of models account for the dependence of the force, and hence the packaging free energy (ΔF), on the loaded DNA length, but differ markedly in interpreting their origin. While DNA confinement entropy is a dominant contribution to ΔF in the MD simulations, in the CT theories this role is fulfilled by interstrand repulsion, and there is no explicit entropy term. The goal of this letter is to resolve this apparent contradiction, elucidate the origin of the entropic term in the MD simulations, and point out its tacit presence in the CT treatments.
    背景与目标: : 受新颖的单分子和块状溶液测量的启发,DNA包装成噬菌体衣具所涉及的力和压力的物理学成为许多最近理论模型的焦点。它们分为两大类: 连续弹性理论 (CT) 和模拟研究-主要是分子动力学 (MD) 类型。两种类型的模型都考虑了力的依赖性,因此也考虑了包装自由能 (Δ f) 对加载的DNA长度的依赖性,但在解释其起源方面存在明显差异。虽然DNA限制熵是MD模拟中对 Δ f的主要贡献,但在CT理论中,此作用是通过链间排斥来实现的,并且没有明确的熵项。这封信的目的是解决这一明显的矛盾,阐明MD模拟中熵项的起源,并指出其在CT治疗中的默认存在。
  • 【具有残基类型特定介电常数的蛋白质-蛋白质结合自由能-相互作用熵的准确有效计算。】 复制标题 收藏 收藏
    DOI:10.1021/acs.jcim.8b00248 复制DOI
    作者列表:Liu X,Peng L,Zhang JZH
    BACKGROUND & AIMS: :Accurate and efficient computation of protein-protein binding free energy remains a grand challenge. In this study, we develop a new strategy to achieve efficient calculation for total protein-protein binding free energies with improved accuracy. The new method combines the recently developed interaction entropy method for efficient computation of entropic change together with the use of residue type-specific dielectric constants in the framework of MM/GBSA to achieve optimal result for protein-protein binding free energies. The new strategy is shown to be computationally efficient and accurate than that using standard MM/GBSA methods in which the entropic computation is performed by the normal model approach and the protein interior is represented by the standard dielectric constant (typically set to 1), both in terms of accuracy and computational efficiency. Our study using the new strategy on a set of randomly selected 20 protein-protein binding systems produced an optimal dielectric constant of 2.7 for charged residues and 1.1 for noncharged residues. Using this new strategy, the mean absolute error in computed binding free energies for these 20 selected protein-protein systems is significantly reduced by more than 3-fold while the computational cost is reduced by more than 2 orders of magnitude, compared to the result using standard MM/GBSA method with the normal mode approach. A similar improvement in accuracy is confirmed for a test set consisting of 10 protein-protein systems.
    背景与目标: : 准确有效地计算蛋白质-蛋白质结合自由能仍然是一个巨大的挑战。在这项研究中,我们开发了一种新策略,以提高准确性来实现对总蛋白质-蛋白质结合自由能的有效计算。新方法结合了最近开发的相互作用熵方法,可有效计算熵变化,并在MM/GBSA框架内使用残基类型特定的介电常数,以实现蛋白质-蛋白质结合自由能的最佳结果。与使用标准MM/GBSA方法相比,新策略在计算上高效且准确,在标准MM/GBSA方法中,熵计算由正常模型方法执行,蛋白质内部由标准介电常数表示 (通常设置为1),在准确性和计算效率方面。我们对一组随机选择的20种蛋白质-蛋白质结合系统使用新策略进行的研究产生了带电残基的最佳介电常数为2.7,非带电残基的最佳介电常数为1.1。使用这种新策略,这20个选定的蛋白质-蛋白质系统的计算结合自由能的平均绝对误差显着降低了3倍以上,而计算成本降低了2个数量级以上,与标准MM/GBSA方法和正常模式方法的结果进行了比较。对于由10个蛋白质-蛋白质系统组成的测试集,也证实了准确性的类似提高。
  • 【准平衡加热对高熵合金空位和异质晶格畸变的元素影响。】 复制标题 收藏 收藏
    DOI:10.1038/s41598-019-51297-4 复制DOI
    作者列表:Huang EW,Chou HS,Tu KN,Hung WS,Lam TN,Tsai CW,Chiang CY,Lin BH,Yeh AC,Chang SH,Chang YJ,Yang JJ,Li XY,Ku CS,An K,Chang YW,Jao YL
    BACKGROUND & AIMS: :We applied Simmons-Balluffi methods, positron measurements, and neutron diffraction to estimate the vacancy of CoCrFeNi and CoCrFeMnNi high-entropy alloys (HEAs) using Cu as a benchmark. The corresponding formation enthalpies and associated entropies of the HEAs and Cu were calculated. The vacancy-dependent effective free volumes in both CoCrFeNi and CoCrFeMnNi alloys are greater than those in Cu, implying the easier formation of vacancies by lattice structure relaxation of HEAs at elevated temperatures. Spatially resolved synchrotron X-ray measurements revealed different characteristics of CoCrFeNi and CoCrFeMnNi HEAs subjected to quasi-equilibrium conditions at high temperatures. Element-dependent behavior revealed by X-ray fluorescence (XRF) mapping indicates the effect of Mn on the Cantor Alloy.
    背景与目标: : 我们应用Simmons-Balluffi方法,正电子测量和中子衍射来估计以Cu为基准的CoCrFeNi和CoCrFeMnNi高熵合金 (HEAs) 的空位。计算了hea和Cu的相应形成焓和相关熵。CoCrFeNi和CoCrFeMnNi合金中的空位依赖性有效自由体积均大于Cu中的空位,这意味着在高温下hea的晶格结构弛豫更容易形成空位。空间分辨的同步加速器x射线测量揭示了CoCrFeNi和CoCrFeMnNi hea在高温下处于准平衡条件下的不同特性。X射线荧光 (XRF) 映射揭示的元素依赖性行为表明Mn对Cantor合金的影响。

+1
+2
100研值 100研值 ¥99课程
检索文献一次
下载文献一次

去下载>

成功解锁2个技能,为你点赞

《SCI写作十大必备语法》
解决你的SCI语法难题!

技能熟练度+1

视频课《玩转文献检索》
让你成为检索达人!

恭喜完成新手挑战

手机微信扫一扫,添加好友领取

免费领《Endnote文献管理工具+教程》

微信扫码, 免费领取

手机登录

获取验证码
登录